myExperiment:Towards Research Objects

David De Roure

Building Linked Web Communities in Biomedicine to Accelerate Research

• What is it?• How it’s being used• How we built it• Towards the e-Laboratory

scientists

LocalWeb

Repositories

Graduate Students

Undergraduate Students

Virtual Learning Environment

Technical Reports

Reprints

Peer-Reviewed Journal &

Conference Papers

Preprints &

Metadata

Certified Experimental

Results & Analyses

experimentation

Data, Metadata Provenance WorkflowsOntologies

Digital Libraries

The social process of Science 2.0

http://usefulchem.wikispaces.com/page/code/EXPLAN001http://www.microsoft.com/mscorp/tc/trident.mspx

http://www.mygrid.org.uk/tools/taverna/

Sharing pieces of processSharing pieces of process

Workflows are the new rock and roll

Machinery for coordinating the execution of (scientific) services and linking together (scientific) resources

The era of Service Oriented Applications

Repetitive and mundane boring stuff made easier

E. Science laboris E. Science laboris

Kepler

Triana

BPEL

Ptolemy II

Taverna

Trident

BioExtract

Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle

Paul meets Jo. Jo is investigating Whipworm in mouse.

Jo reuses one of Paul’s workflow without change.

Jo identifies the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite.

Previously a manual two year study by Jo had failed to do this.

Reuse, Recycling, RepurposingReuse, Recycling, Repurposing

“Facebook for Scientists” ...but different to Facebook!

A repository of research methods

A community social network A Virtual Research

Environment

Open source (BSD) Ruby on Rails application with HTML, REST and SPARQL interfaces

Project started March 2007 Closed beta since July 2007 Open beta November 2007

myExperiment currently has 1712 registered users, 141 groups, 584 Taverna workflows plus 81 others, and 51 packsGo to www.myexperiment.org to access publicly available content or create an account

User Profiles Groups Friends Sharing Tags Workflows Developer interface Credits and Attributions Fine control over privacy Packs Federation Enactment

myExperiment FeaturesmyExperiment FeaturesD

istin

ctiv

es

Control over sharingControl over sharing

The most important aspect of myExperimentDesigned by scientists

The most important aspect of myExperimentDesigned by scientists

ResultsLogs

Results

Metadata PaperSlides

Workflow 16

Workflow 13

Common pathways

QTL

A PackA Pack

For DevelopersFor Developers

All the myExperiment services are accessible through simple RESTful programming interfaces use your existing environment and augment it with

myExperiment functionality build entirely new interfaces and functionality

mashups The Ruby on Rails codebase is open source (BSD) so

you can run your own myExperiment – perhaps for your own lab or to develop new funcionality

Go to wiki.myexperiment.org for information about our Developer Community

• What is it?• How it’s being used• How we built it• Towards the e-Laboratory

Adam Belloum

WS-VLAM composerHuman transcriptome map

discovered RIDGE

Human transcriptome map

More details: http://staff.science.uva.nl/~inda/SigWin-detector.html

DNA curvature of the Escherichia Coli chromosome

SigWin-detector: is a grid-enabled workflow application that takes a sequence of numbers and a series of window sizes as input and detects all significant windows for each window size using a moving median false discovery rate (mmFDR) procedure.

Carol Lushbough

Google GadgetsGoogle Gadgets

Bringing myExperiment to the iGoogle userBringing myExperiment to the iGoogle user

Taverna PluginTaverna Plugin

Bringing myExperiment to the Taverna userBringing myExperiment to the Taverna user

FacebookFacebook

• Of the 661 workflows, 531 are publicly visible whereas 502 are publicly downloadable.

• 3% of the workflows with restricted access are entirely private to the contributor and for the remaining they elected to share with individual users and groups.

• 69 workflows (over 10%) have been shared, with the owner granting edit permissions to specific users and groups.

• In addition there are 52 instances where users have noted that a workflow is based on another workflow on the site.

• The most viewed workflow has 1566 views.• There are 50 packs, ranging from tutorial examples to

bundles of materials relating to specific experiments.

CScientists do share! Scientists do share!

Consumers > Curators > Producers

• Supermarket shoppers Workflow consumers prefer larger workflows ready to be downloaded and enacted

• Tool buildersWorkflow authors prefer smaller, modularized workflows which can be assembled & customized

• Quality and sufficiency of good documentation

• Content decay surveillance

• Consumers > curators > producers

• Contributor, expert and community curation

• Incentives for curation

AnalysisAnalysis

Two distinct myExperiment communities:

Considerations in Collaborative Curation:

• What is it?• How it’s being used• How we built it• Towards the e-Laboratory

24/5/2007 | myExperiment | Slide 28

Search Engine

reviewsratingsgroupsfriendships

tags

Enactor

filesworkflows

`

HTML

For DevelopersFor Developers

RDF Store

SPAR

QL

endp

oint

Managed REST API

face

book

iGoo

gle

andr

oid

XML

APIconfig

mySQL

profiles

packscredits

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX myexp: <http://rdf.myexperiment.org/ontology#>PREFIX sioc: <http://rdfs.org/sioc/ns#>select ?friend1 ?friend2 ?acceptedat where {?z rdf:type<http://rdf.myexperiment.org/ontology#Friendship> . ?z myexp:has-requester?x .?x sioc:name ?friend1 . ?z myexp:has-accepter ?y . ?y sioc:name ?friend2 .?z myexp:accepted-at ?acceptedat }

All accepted Friendships including accepted-at time Semantically-Interlinked

Online Communities

SPARQL endpointSPARQL endpoint

http://rdf.myexperiment.org/Aggregation/Pack/56

Exporting packsExporting packs

Communications of the ACM 51, 4 (Apr. 2008), 52-58

Scientific Discourse Relationships Ontology Specification

Open Provenance Model

Phase 2• Repository integration (institutional:

EPrints, Fedora)• Controlled vocabularies• Relationships between items (in and

between packs)• Recommendations• Improved search ranking and faceted

browsing• Indexing of packs• New contribution types (Meandre,

Kepler, e-books)• Further blog / wiki integration• Biocatalogue integration

Phase 2Phase 2

Workflows and Services

Experts

Social by User Community

refinevalidate

refinevalidate

Self by Service Providers

seed seed

refinevalidate

seed

Automated

refinevalidate seed

Content Capture and CurationReuse and SymbiosisReuse and Symbiosis

1. Fit in, Don’t Force Change2. Jam today and more jam

tomorrow

3. Just in Time and Just Enough

4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects

1. Fit in, Don’t Force Change2. Jam today and more jam

tomorrow

3. Just in Time and Just Enough

4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects

Six Principles of Software Design to Empower ScientistsSix Principles of Software Design to Empower Scientists

1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger

Picture4. Favours will be in your

Favour5. Know your users6. Expect and Anticipate

Change

1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger

Picture4. Favours will be in your

Favour5. Know your users6. Expect and Anticipate

Change

De Roure, D. and Goble, C. "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp. 88-95, January/February 2009

• What is it?• How it’s being used• How we built it• Towards the e-Laboratory

e-Laboratory Lifecyclee-Laboratory Lifecycle Local projects using Taverna and/or myExperiment

SysMO

Ondex

NEMA

Obesity eLab

Shared Genomics

CombeChem

LifeGuide

IBBRE

• A laboratory is a facility that provides controlled conditions in which scientific research, experiments and measurements may be performed, offering a work space for researchers.

• An e-Laboratory is a set of integrated components that, used together, form a distributed and collaborative space for e-Science, enabling the planning and execution of in silico experiments -- processes that combine data with computational activities to yield experimental results

What is an e-Laboratory?What is an e-Laboratory?

• An e-Lab consists of:1. a community2. work objects3. generic resources for building and transforming work

objects

• Sharing infrastructure and content across projects

e-Labse-Labs

• An e-Lab is built from a collection of services, consuming and producing Research Objects

RO Bus

Service Service Service

Workbench/RO driven UI

RO awareservices

Service

VisualisationNotification

Annotation etc.

e-Labs + Research Objectse-Labs + Research Objects

1st Generation

Current practice of early adoptors of e-Labs tools such as Taverna

Characterised by researchers using tools within their particular problem area, with some re-use of tools, data and methods within the discipline.

Traditional publishing is supplemented by publication of some digital artefacts like workflows and links to data.

Provenance is recorded but not shared and re-used.

Science is accelerated and practice beginning to shift to emphasise in silico work

2nd Generation

Designing and delivering now, e.g. Obesity e-Lab

Experience with Taverna and myExperiment and on our research results arising from these activities

Key characteristic is re-use - of the increasing pool of tools, data and methods across areas/disciplines.

Contain some freestanding, recombinant, reproducible research objects. Provenance analytics plays a role.

New scientific practices are established and opportunities arise for completely new scientific investigations.

3rd GenerationThe vision - the e-Labs we'll be delivering in 5 years - illustrated by open science.Characterised by global reuse of tools, data and methods across any discipline, and surfacing the right levels of complexity for the researcher. Key characteristic is radical sharing Research is significantly data driven - plundering the backlog of data, results and methods. Increasing automation and decision-support for the researcher - the e-Laboratory becomes assistive. Provenance assists designCuration is autonomic and social

e-Laboratory Evolutione-Laboratory Evolution

Workflow Monitoring

Event Logging

Social Metadata

Annotation Service

Search, ranking

User Registration

Distributed Data Query

Job ExecutionNaming and Identity

Anonimisation

Text Mining

Research ObjectManagement

Probity

Coreference Resolution

Assembling e-LaboratoriesAssembling e-Laboratories Example Core Services

An e-Lab is a set of components and resources An open system, not a software

monolith Utility of components

transcends their immediate application

We envisage an ecosystem of cooperating e-Laboratories

What are the e-Lab components and services?

What are the Research Objects?

ResultsLogs

Results

Metadata PaperSlides

Feeds into

produces

Included in

produces Published in

produces

Included in

Included in

Included in

Published in

Workflow 16

Workflow 13

Common pathways

QTLPaul Fisher

David Shotton

Anatomy of a Research ObjectAnatomy of a Research Object

SWAN-SIOC

Experiments

myExperiment

Tim Clark

1. Composite. Contain typed interrelationships and dependencies between resources but are in turn labelled and identifiable as an individual resource.

2. Distributed. Structured collections of references to locally managed and externally located resources. Implications for reliability, consistency, mixed stewardship, versioning and identity resolution.

3. Annotated. Carry metadata concerning provenance profile, lifecycle profile, sharing profile (permissions, licensing, downloads, views), curation profile (tags, comments, ratings) and usage profile.

4. Repeatable. Capture information about the lifecycle of the investigation facilitating experiments to be repeatable (without change), reusable (with reconfiguration), replayable and/or repurposable (as new components or templates).

5. Interoperable. Publishable and exchangeable units that facilitate interoperability; OAI-ORE standards increase interoperability and facilitate the consumption of Research Objects in between applications.

Characteristics of a Research ObjectCharacteristics of a Research Object

ThoughtsThoughts

myExperiment provides social infrastructure – it facilitates sharing and enables scientists to “collaborate in order to compete”

myExperiment has growing community and growing content New content types: meandre, kepler, R, matlab, ...,

spreadsheets? SPARQL queries? We are targetting how we believe research will be

conducted in the future, through the assembly of e-Laboratories which share Research Objects

SPARQL endpoint is an effective alternative to the API – provides any service you want!

Workflows for Semantic Web scripting?

Contact

David De Rouredder@ecs.soton.ac.uk

Carole Goblecarole.goble@manchester.ac.uk

Slide Credits

Simon Coles, Paul Fisher, Adam Belloum,Sean Bechhofer, David Shotton